#MD01_2412.Harada.2006

---
title: "MD01_2412.Harada.2006"
output: 
  flexdashboard::flex_dashboard:
    vertical_layout: scroll
    theme: bootstrap
    source_code: embed
    orientation: rows
---

```{r setup, include = FALSE}
library(flexdashboard)
library(maptools)
library(tidyverse)
library(purrr)
library(leaflet)
library(plotly)
library(lipdR)
library(dygraphs)
library(geoChronR)
library(lipdverseR)
#read functions
load("../../temp.Rdata")
load("../../chronTemp.Rdata")


#remove columns we don't want to plot
varNames <- sapply(TS, "[[","paleoData_variableName")

# good <- which(!(varNames %in% c("year","depth","age")))
# TS <- TS[good]



#All datasets
dsn <- lipdR::pullTsVariable(TS,"dataSetName")
ui <- which(!duplicated(dsn))
udsn <- dsn[ui]
lat <- lipdR::pullTsVariable(TS,"geo_latitude")[ui]
lon <- lipdR::pullTsVariable(TS,"geo_longitude")[ui]
elev <- lipdR::pullTsVariable(TS,"geo_elevation")[ui]


archiveType <- lipdR::pullTsVariable(TS,"archiveType")[ui]
link <- paste0(udsn,".html") %>%
  str_replace_all("'","_")


#Organize metadata for map
map.meta <- data.frame(dataSetName = udsn, #datasetname
                       lat = lat,#lat
                       lon = lon,#lon
                      # elev = elev,#elevation
                       archiveType = factor(archiveType),#archiveType
                       link = link)#Link


#set index number

i = 385
thisTS <- TS[which(udsn[i] == dsn)]
```
#MD01_2412.Harada.2006

Metadata {.sidebar}
-------------------------------------
[Download LiPD file](MD01_2412.Harada.2006.lpd)
            

[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/MD01_2412.Harada.2006.lpd)
            

[Download paleoData only (csv)](MD01_2412.Harada.2006.csv)
            

[Download chronData only (csv)](MD01_2412.Harada.2006-chron.csv)
            

[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)


root
archiveType: MarineSediment
originalDataUrl: www.ncdc.noaa.gov/paleo/study/9096
lipdVersion: 1.3


pub

pub1
author: list(list(name = "Harada, Naomi; Ahagon, Naokazu; Sakamoto, Tatsuhiko; Uchida, Masao; Ikehara, Minoru; Shibata, Yasuyuki"))
citeKey: KUFYKK47
journal: Global and Planetary Change
volume: 53
pages: 29   46
title: Rapid fluctuation of alkenone temperature in the southwestern Okhotsk Sea during the past 120 ky


pub2



geo
latitude: 44.5275
longitude: 145.004
elevation: -1225
siteName: MD01_2412


PaleoData columns

depth (cm)
TSid: T2L_MD01_2412_depth
variableName: depth
units: cm
description: Sample depth


ageDuplicate (cal years BP)
TSid: T2L_MD01_2412_age_median
variableName: ageDuplicate
units: cal years BP
description: Median age


ageOriginal (BP)
TSid: T2L_MD01_2412_age_original
variableName: ageOriginal
units: BP
description: Original age


ageMedianBacon (cal years BP)
TSid: T2L_MD01_2412_age_medianMedianBacon
variableName: ageMedianBacon
units: cal years BP
description: Median age


age (BP)
TSid: T2L_MD01_2412_age
variableName: age
units: BP
description: Original age


temperature (degC)
TSid: T2L_MD01_2412_uk37_SST_from_uk37
variableName: temperature
units: degC
description: SST calculated from uk37

interpretation

1
direction: positive
variable: T
scope: climate
variableGroup: Temperature
variableGroupOriginal: T
seasonality: annual
seasonalityGeneral: annual
seasonalityOriginal: 1 2 3 4 5 6 7 8 9 10 11 12
variableDetail: sea@surface
variableGroupDirection: list("negative")




Uk37 (unitless)
TSid: T2L_MD01_2412_uk37
variableName: Uk37
units: unitless


ChronData columns

depth_top (cm)
TSid: T2L_MD01_2412_depth_top
variableName: depth_top
units: cm
description: Sample top depth


depth_bottom (cm)
TSid: T2L_MD01_2412_depth_bottom
variableName: depth_bottom
units: cm
description: Sample bottom depth


age_type (unitless)
TSid: RC3BPGwHVg7
variableName: age_type
units: unitless


age (yr BP)
TSid: RbW0YiuMOmH
variableName: age
units: yr BP


labcode ()
TSid: T2L_MD01_2412_labcode
variableName: labcode
description: Lab sample code


mat_dated ()
TSid: T2L_MD01_2412_mat_dated
variableName: mat_dated
description: Material dated


c14_date (RC yr BP)
TSid: T2L_MD01_2412_c14_date
variableName: c14_date
units: RC yr BP
description: 14C date


c14_1s_err (RC yr BP)
TSid: T2L_MD01_2412_c14_1s_err
variableName: c14_1s_err
units: RC yr BP
description: 14C 1-sigma error


delta_r ()
TSid: T2L_MD01_2412_delta_r
variableName: delta_r
description: delta R


delta_r_original ()
TSid: T2L_MD01_2412_delta_r_original
variableName: delta_r_original
description: Original delta R


delta_r_1s_error ()
TSid: T2L_MD01_2412_delta_r_1s_error
variableName: delta_r_1s_error
description: delta R 1-sigma error


delta_r_1s_error_original ()
TSid: T2L_MD01_2412_delta_r_1s_error_original
variableName: delta_r_1s_error_original
description: Original delta R 1-sigma error


other_date ()
TSid: T2L_MD01_2412_other_date
variableName: other_date
description: Other date


other_1s_err ()
TSid: T2L_MD01_2412_other_1s_err
variableName: other_1s_err
description: Other date 1-sigma error


other_type ()
TSid: T2L_MD01_2412_other_type
variableName: other_type
description: Other date type


Row {.tabset .tabset-fade}
-----------------------------------------------------------------------

### Sitemap

```{r}
  map.meta.split <- split(map.meta, map.meta$archiveType)


factpal <- colorFactor("Paired",map.meta$archiveType)
buff <- 15
l <- leaflet() %>% 
  addTiles() %>% 
  fitBounds(map.meta$lon[i]-buff,map.meta$lat[i]-buff,map.meta$lon[i]+buff,map.meta$lat[i]+buff)
  

  
  
names(map.meta.split) %>%
  purrr::walk( function(df) {
    l <<- l %>%
      addMarkers(data=map.meta.split[[df]],
                 lng=~lon, lat=~lat,
                 label=~as.character(archiveType),
                 popup=~paste(str_c('Dataset: ',dataSetName,''),
                                 # str_c("Elevation: ",elev),
                                  str_c("Archive Type: ",archiveType),
                                  sep = "
"),
                 group = df,
                 clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F),
                 labelOptions = labelOptions(noHide = F,
                                             direction = 'auto'))
  })

l <- l %>%   addCircleMarkers(lng = map.meta$lon[i], lat = map.meta$lat[i],radius = 20,color = "red",fillColor = "none")

l %>%
  addLayersControl(position = "bottomleft",
    overlayGroups = names(map.meta.split),
    options = layersControlOptions(collapsed = FALSE,
                                   opacity = 0.8)
  )
```

### Search the LiPDverse (Beta! doesn't work well yet)
```{r}
#Add google search bar
htmltools::includeHTML("../../googleSearchChunk.html")
```


Row {.tabset .tabset-fade}
-----------------------------------------------------------------------

### temperature (degC)
```{r}
plotCol(thisTS,ind = 5)
```

### Uk37 (unitless)
```{r}
plotCol(thisTS,ind = 4)
```

Row {.tabset .tabset-fade}
-----------------------------------------------------------------------

### depth_top (cm)
```{r}
plotCol(chronTS,ind = 2)
```

### depth_bottom (cm)
```{r}
plotCol(chronTS,ind = 3)
```

### age_type (unitless)
```{r}
plotCol(chronTS,ind = 14)
```

### age (yr BP)
```{r}
plotCol(chronTS,ind = 15)
```

### labcode ()
```{r}
plotCol(chronTS,ind = 1)
```

### mat_dated ()
```{r}
plotCol(chronTS,ind = 4)
```

### c14_date (RC yr BP)
```{r}
plotCol(chronTS,ind = 5)
```

### c14_1s_err (RC yr BP)
```{r}
plotCol(chronTS,ind = 6)
```

### delta_r ()
```{r}
plotCol(chronTS,ind = 7)
```

### delta_r_original ()
```{r}
plotCol(chronTS,ind = 8)
```

### delta_r_1s_error ()
```{r}
plotCol(chronTS,ind = 9)
```

### delta_r_1s_error_original ()
```{r}
plotCol(chronTS,ind = 10)
```

### other_date ()
```{r}
plotCol(chronTS,ind = 11)
```

### other_1s_err ()
```{r}
plotCol(chronTS,ind = 12)
```

### other_type ()
```{r}
plotCol(chronTS,ind = 13)
```